Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes
John F. Thompson,Arthur Landy +1 more
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An empirical relation between the degree of bending and the altered electrophoretic mobility in polyacrylamide gels that allows estimation of protein-induced bends is generated.Abstract:
Protein-induced DNA bending is an important element in the structure of many protein-DNA complexes, including those involved in replication, transcription, and recombination. To understand these structures, the path followed by the DNA in each complex must be established. We have generated an empirical relation between the degree of bending and the altered electrophoretic mobility in polyacrylamide gels that allows estimation of protein-induced bends. This technique has been used to analyze 17 different protein-DNA complexes formed by six proteins including the four proteins involved in lambda site-specific recombination. The simplicity of this technique should make it useful in estimating angles for the construction of models of protein-DNA complexes and readily applicable to many systems where questions of higher-order structure are important for understanding function.read more
Citations
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SOX9 is a potent activator of the chondrocyte-specific enhancer of the pro alpha1(II) collagen gene.
TL;DR: The results strongly suggest a model whereby SOX9 is involved in the control of the cell-specific activation of COL2A1 in chondrocytes, an essential component of the differentiation program of these cells.
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Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.
TL;DR: The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees.
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Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors.
TL;DR: The electron-transport chains of Escherichia coli are composed of many different dehydrogenases and terminal reductases (or oxidases) which are linked by quinones (ubiquinone, menaquinone and demethylmenaquinone); Quinol:cytochrome c oxido-reductase ('bc1 complex') is not present.
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The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures
TL;DR: Evidence is provided that DNA binding by the HMG domain of LEF-1 involves primarily minor groove contacts and induces a bend of approximately 130 degrees in the DNA helix, which suggests that H MG domain proteins can serve as "architectural" elements in the assembly of higher-order nucleoprotein structures.
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TRF1 is a dimer and bends telomeric DNA
TL;DR: It is shown that TRF1 binds DNA as a dimer using a large conserved domain near the N‐terminus of the protein for TRF2–TRF1 interactions, suggesting that DNA bending is important for the function of telomeres in yeast and mammals.
References
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The locus of sequence-directed and protein-induced DNA bending
Hen-Ming Wu,Donald M. Crothers +1 more
TL;DR: The bending locus of trypanosome kinetoplast DNA, identified by gel electrophoresis, has tracts of a simple repeat sequence symmetrically distributed about it, with a repeat interval of 10 base pairs.
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DNA bending at adenine . thymine tracts.
TL;DR: Intrinsic bending of DNA molecules results from local structural polymorphism in regions of homopolymeric dA · dT which are at least 4 base pairs long; the A · T tracts must be repeated in phase with the helix screw.
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The structure of an oligo(dA)·oligo(dT) tract and its biological implications
TL;DR: The crystal structure of a B-type DNA dodecamer containing a homopolymeric run of six A·T base pairs shows that this region possesses special structural features, including a system of bifurcated hydrogen bonds, which explains some of the properties of this simple homopolymer.
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Structure of the nucleosome core particle at 7 Å resolution
TL;DR: The crystal structure of the nucleosome core particle has been solved to 7 A resolution as discussed by the authors, and the right-handed B-DNA superhelix on the outside contains several sharp bends and makes numerous interactions with the histone octamer within.